5 speed is the way to go on the 2.0, this car is not tuned for top end. All the torque is in the middle, short shift it and you'll get the most out of it plus your MPG won't suffer much. My mods were done on the cheap, mostly junk yard parts and second hand:
Audio:
Dual blue tooth hands free stereo (sounds not so great, but better than getting a ticket for using my cell and it was dirt cheap)
Pioneer 6x8 two way speakers x 4 (should have saved up for some better speakers)
Kicker 10inch sub sealed box (cheap box, cheap sub, not trying to win any audio competitions)
Dual 400 watt amp (bridged) (walmart FTW, pushes my clearance 10inch pretty good)
Iinterior:
Mystique gauge cluster with tachometer (a must for the content deprived contour GL's)
Mystique map light (why didn't they all come with this?)
Mystique dual cup holder (searched for days before I found one that was shallow enough for my center console)
Mystique headliner handles rear (don't know why I did this but it only cost a couple of bucks)
Mystique passenger front seat (there are pockets in the rear of these seats if it matters, the padding is so much better than the stock GL's)
Mystique drivers side 10 way adjustable power seat (most cars will already have the harness for this under their drivers seat, you may need to add a fuse for it though)
Mystique fold down rear seat w/arm rest/trunk pass through
Rearcenter console cigarettes lighter (a little hack I decided to add for a road trip, much better than one of those cigarette lighter splitters)
Suspension\brakes:
1999 Ford Contour SE 17mm rear sway bar (couldn't find an 18mm and this thing cost next to nothing and made a noticeable improvement in cornering)
1999 Ford Contour SE 15inch wheels gloss black 205 6015's (look surprisingly good on a lowered contour and I paid $54 from the junk yard)
1996 Mystique rear disc brakes (got these on the cheap from the JY, some new e brake cables for the rear disc equipped cars and I couldn't have been happier)
Performance:
Accel coil pack
Esslinger under drive pulley
Exterior:
HID low beams (I know how we all feel about this but I need to see at night, beam scatter and oncoming drivers be damned!)
B&G lowering springs (picked up on this forum for $75 if I recall correctly, love them, love the way the car sits)
Walmart Fog lights (they're not the best you can get but they work and are aesthetically more pleasing than the black place holders)
Modifications acquired not yet installed
Alternator over drive pulley
Walbro 190lph fuel pump
Accel Adjustable FPR (you'll need to use a CAI if you want to use the accel FPR, it won't clear the stock plastic manifold)
1999 Ford Contour SE trunk lid w/spoiler (I'm not in love with the spoiler, might have to go with a mystique trunk lid and just swap on the contour center light)
1999 Ford Contour SE side skirts (JY find, $5!! I'll need to get a riveter from Harbor Freight)
This has been a gratifying car to own, roll up windows and manual locks. Power windows and locks are the only thing that I miss having. However if its about just back to basics driving, low weight, fun handling car.... I never wanted a V6 powered contour. I paid $1100 for this car when it had 53k on the odo. Its got around 198k on it now, no harness problems, original clutch. I did the timing, replaced the water pump, alternator and AC compressor, catalytic converter and a rear wheel bearing since I've owned the car. I had a strange issue with the clutch master cylinder, I think that worn rear brake shoes on my drums was introducing contamination into the fluid via an over extended cylinder. I wrecked it and replaced the whole front end for about $150 worth of junk yard parts. If you wrench on your car and have a solid car to begin with these cars will give you years of trouble free ownership, cheap maintenance costs and with a few suspension mods a very rewarding driving experience.